Raman studies of nucleic acids. XII. Conformations of oligonucleotides and deuterated polynucleotides

Abstract

SynopsisLaser Raman spectra of the trinucleoside diphosphate ApApA and dinucleoside phosphates ApU, UpA, GpC, CpG, and GpU are reported and discussed. Assignments of conformationally sensitive frequencies are. facilitated by comparison with spectra reported here of poly(rA), poly(rC), and poly(rU) in deuterium oxide solutions. The significant spectral differences between ApU and UpA, and between GpC and CpG, reveal that the sequence isomers have nonidentical conformations in aqueous solution. In UpA a t low temperature the bases are stacked and the backbone conformation is similar to that found in ordered polynucleotide structures and RNA. In ApU no base stacking can be detected and the backbone conformation differs from that found in UpA, both in the orientation of phosphodiester linkages and in the internal conformation of ribose. At the conditions employed neither ApU nor UpA exhibits base pairing in aqueous solutions. In both GpC and CpG the bases are stacked and the phosphodiester conformations are similar to those encountered for UpA and RNA. However, major differences between spectra of GpC and CpG indicate that the geometries of stacking and ribosyl conformations are different. In GpC the Raman data favor the formation of hydrogen bonded dimers containing GC pairs. Protonation of C in GpC is sufficient to eliminate the ordered conformation detected by Raman spectroscopy. Despite the ordered backbone conformation evident in GpU, this dinucleoside apparently contains neither stacked nor hydrogen bonded bases at the conditions employed here. The Raman data also confirm the stacking interactions in ApApA, poly(rA), and poly(rC) but suggest that the backbone conformation in poly(rC) differs qualitatively from that found in most ordered polynucleotide structures and is thermally more stable. The present results demonstrate the sensitivity of the Raman technique to sequence-related structural differences in oligonucleotides and provide additional spectra-structure correlations for future conformational studies of RNA by laser Raman spectroscopy.

Minimum energy conformations of DNA dimeric subunits: Potential energy calculations for dGpdC, dApdA, dCpdC, dGpdG, and dTpdT

“…On the other hand, solution studies of UpA have shown that the predicted w',w = g-,g-global minimum is, in fact, the predominant conformer there. 49 Possibly, a similar situation may occur for pdTpdT in solution.…”

Raman spectra and structure of a 25mer HCV RNA

“…This is consistent with the fact that Raman spectra of polyribocytidylic acid and polyriboadenylic acid show the formation of ordered single-stranded structure at neutral pH with stacked bases and a backbone geometry of the A-type. [17,18] In addition, single-stranded heterogeneous sequences in RNA adopt this type of backbone conformation. [29] In the Raman spectrum of this HCV RNA a shoulder located near 828 cm −1 (Table 1) is visible which can be generated by the B backbone form on the basis of the above spectrum-structure correlation.…”

“…Base-paired uracil shows a strong band near 1680 cm −1 , [14] whereas the νC O intensity maximum shifts toward 1665 cm −1 in nonpaired residues. [17,32] Concerning the Raman bands below 1650 cm −1 , these can be assigned to cytosine and adenine bases. [14,17] Given that the 1699 cm −1 band corresponds to base-paired guanine residues, the intensity of this band relative to the ν s PO 2 − intensity at 1098 cm −1 can provide the proportion of guanine residues that are Watson-Crick base-paired.…”

“…[17,32] Concerning the Raman bands below 1650 cm −1 , these can be assigned to cytosine and adenine bases. [14,17] Given that the 1699 cm −1 band corresponds to base-paired guanine residues, the intensity of this band relative to the ν s PO 2 − intensity at 1098 cm −1 can provide the proportion of guanine residues that are Watson-Crick base-paired. In order to estimate as accurately as possible maxima and intensities of the bands in the 1725-1600 cm −1 region, a band decomposition is presented in Fig.…”

Thermodynamics of single strand DNA base stacking

“…14 Furthermore, the directionality of the doublet is important in that UpA is stacked at low temperature, whereas ApU is not stacked and the backbone conformation of ApU differs from that found in UpA. 14 However, based on the ssDNA sequences of this investigation and the restraints just described the stacking of ssDNA sequences may be initiated by a unique nucleation quadruplet site in the sequence. The effect of salt on the stability arises purely out of entropic effects since the two-state A,B transition temperatures change, while the transition enthalpies remain essentially the same for each sequence.…”